Interpretive Summary: Roots are a vital organ for absorbing soil moisture and nutrients and influencing drought resistance. The identification of DNA markers associated with quantitative root traits may allow the estimation of parameters of genetic architecture and improve root traits by DNA molecular marker-assisted selection (MAS). A mapping population of 120 recombinant inbred lines (RILs) derived from a cross between japonica upland rice ‘IRAT109’ and paddy rice ‘Yuefu’ was used in this research. All plant materials were grown in PVC-pipe. We measured the root traits including basal root thickness (BRT), root number (RN), maximum root length (MRL), root fresh weight (RFW), root dry weight (RDW) and root volume (RV) in seedling (I), tillering (II), heading (III), grain filling (IV) and mature (V) stages, respectively. Phenotypic correlations showed that BRT had a significant positive correlation with MRL at the majority of stages, and no correlation with RN. MRL had no correlation with RN except at the seedling stage. BRT, MRL and RN had a significant positive correlation with RFW, RDW and RV in all growth stages. The results indicated that the additive effects played main roles for BRT, RN and MRL, whereas effects of interaction between genes were important for RFW, RDW and RV. Environment effect also played important roles in controlling root traits. A total 84 additive-effect quantitative trait loci (QTL) and 86 pairs of interactions were detected for the six root traits at five stages. Only 12 additive QTL were expressed in at least two periods. This indicated that the majority of QTL was specific for developmental stage. Two main effect QTL were detected at the heading stage and explained 19% and 10%, respectively, of the total phenotypic variation in BRT without any influence from environments. These QTL can be used in breeding programs for improving root traits.

Technical Abstract:
Roots are a vital organ for absorbing soil moisture and nutrients and influencing drought resistance. The identification of quantitative trait loci (QTL) with molecular markers may allow the estimation of parameters of genetic architecture and improve root traits by molecular marker-assisted selection (MAS). A mapping population of 120 recombinant inbred lines (RILs) derived from a cross between japonica upland rice ‘IRAT109’ and paddy rice ‘Yuefu’ was used for mapping QTL of developmental root traits. All plant materials were grown in PVC-pipe. Basal root thickness (BRT), root number (RN), maximum root length (MRL), root fresh weight (RFW), root dry weight (RDW) and root volume (RV) were phenotyped in seedling (I), tillering (II), heading (III), grain filling (IV) and mature (V) stages, respectively. Phenotypic correlations showed that BRT had a significant positive correlation with MRL at the majority of stages, and no correlation with RN. MRL had no correlation with RN except at the seedling stage. BRT, MRL and RN had a significant positive correlation with RFW, RDW and RV in all growth stages. QTL analyses indicated that the additive effects played main roles for BRT, RN and MRL, whereas epistatic effects were important for RFW, RDW and RV. QTL by environment interaction (Q×E) effect also played important roles in controlling root traits. A total 84 additive-effect QTLs and 86 pairs of epistatic QTLs were detected for the six root traits at five stages. Only 12 additive QTL were expressed in at least two periods. This indicated that the majority of QTL was specific for developmental stage. Two main effect QTL, brt9a and brt9b, were detected at the heading stage and explained 19% and 10%, respectively, of the total phenotypic variation in BRT without any influence from environments. These QTL can be used in breeding programs for improving root traits.